Fig. 6

ASM scores on the CRC dataset. a MDS plot of all the samples in the CRC dataset, based on all the the \(\text{ASM}_{\text{tuple}}\) scores. Scores were square-root transformed before plotting. b MDS plot based on the \(\text{ASM}_{\text{snp}}\) scores. Scores were arcsine transformed. MDS plots were generated with the plotMDS function from limma and the top 1000 most variable positions. N: normal mucosa; C: CRC. Each pair of samples from the 6 patients with CRC is numbered from 1 to 6. c A DAME detected in CIMP CRCs using the \(\text{ASM}_{\text{tuple}}\) score shows a higher signal than using the \(\text{ASM}_{\text{snp}}\) score. Region shown is located on chr9:99,983,697–99,984,022, shaded region in the center corresponds to the DAME. Tracks for methylation levels (meth) and methylation levels in reference and alternative alleles (based on SNP in chr9:99,983,812) are also shown. Points in \(\text{ASM}_{\text{tuple}}\) and meth tracks correspond to intermediate positions between a pair of CpG sites. Points in the rest of tracks correspond to CpG sites. d − log10(p values) at each CpG position, calculated with \(\text{ASM}_{\text{tuple}}\) and \(\text{ASM}_{\text{snp}}\). Black line is drawn at \(-\log10(0.05)\). Sample 4 (C4 and N4) does not appear in the last two tracks because it is not heterozygous at the evaluated SNP